ComSeq

Overview

NEW! (April 2013): The latest version of ComSeq is now available from
GitHub .
The package at the Broad Institute URL will not be updated!

ComSeq is a set of utilities used for simulating and analyzing
compressed-sensing pooling design experiments for
next-generation sequencing projects. The aim is to identify
novel rare alleles, or detect individuals who are carriers of
known SNPs in a large population. The package enables an
in-silico simulation of a sequencing pooling experiments,
including modeling of sequencing error parameters. The package
also enables reconstructing genotypes of individuals profiled
in real experiments. Detailed instructions and usage examples
are given in the README file.

ComSeq Installation

ComSeq includes a set of Matlab functions which can be individually
used. You can download the whole package, or individual
functions below. To install the package simply download the
file comseq.tgz to a directory of your choice, extract it, and
add to your Matlab path. You can also obtain a stand-alone
executible for various platforms upon request.
The package uses the GPSR algorithm. We thank MÃ¡rio Figueiredo for allowing us to include it in this package.

Computes the maximal sample size we can reconstruct for a given number of lanes, or the minimal number of lanes sufficient to reconstruct a certain number of individuals. see optimize_experiment_settings_example.m for an example